A confluence of events, including the sequencing of the human genome and the advances in DNA microarray technology, have created an opportunity to undertake a comprehensive functional genomics analysis of JRA. Such an approach is likely to result in novel insights into the pathophysiology, diagnosis, and therapy of these disorders. While peripheral blood leukocytes (PBL) are more readily accessible than is synovial tissues, PBL may not be fully representative of the pathophysiologic processes responsible for maintenance of arthritis. Direct analysis of synovial tissues is likely to be necessary to elucidate disease-related pathways, as well as to validate the pathophysiologic relevance of peripheral blood gene expression profiles. Furthermore, synoviocytes are likely responsive to mediators secreted by PBL, and vice versa. Preliminary data demonstrate distinct differences in synovial tissue gene expression profiles that differentiate between polyarticular and systemic onset JRA, even after many years of disease, suggesting that the underlying mechanisms responsible for these two disease subtypes persist throughout the course of disease. This proposal is designed to identify the differentially expressed genes in JRA synovial tissue, identify synovial gene expression profiles that differentiate chronic disease in two JRA subtypes (polyarticular and systemic onset), and elucidate the molecular pathways responsible for the invasive phenotype of fibroblasts in arthritic synovium. Using DNA microarrays covering the majority of the human genome, the first Specific Aim will identify the differentially expressed genes in synovium of patients with long-standing JRA, discover novel genes hitherto not known to be involved in JRA, identify specific profiles that differentiate systemic-onset from polyarticular JRA, and compare gene expression profiles from JRA synovium with profiles of PBL and synovial fluid cells derived from other projects in this PO1, including paired PBL samples. The second Specific Aim will elucidate the molecular pathways responsible for the aggressive behavior of fibroblasts in arthritic synovium. These studies will determine the contribution of JRA synovial fibroblasts to the global synovial profile, identify genes differentially expressed in JRA synovial fibroblasts, compared to fibroblasts from non-inflamed synovium, and identify genes from JRA fibroblasts whose expression in culture is stably altered. These studies will result in a comprehensive database to be used as a road map for developing and testing novel hypotheses and for investigating specific pathways and genes in the pathophysiology of JRA. To facilitate this outcome, the database will be made available to the scientific community via the internet.